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Saturday, January 30, 2010

Following Trails of the Cro-Magnon - I

The Cro-Magnon type has tacitly been invoked as the most likely forebearer of contemporary Europeans—where human paleontological record of Europe is concerned—within "Western" academic media circles, the so-called remains having been branded as being that belonging to modern anatomically modern human phylogen. Recently, the Oase 2 cranium finding in Romanian Pes¸tera cu Oase cave setting has culminated into efforts to present another viable alternative to the Cro-Magnon type, as potential forebearers of contemporary Europeans, given that cranio-morphic assessment renders it relatively more modern than the rather incomplete item of the Oase I mandible. However, the Oase 2 is determined to have its own set of peculiarities that distinguish it from modern human examples, whether it happens to be those of the Middle Paleolithic, Early Upper Paleolithic, Middle Upper Paleolithic or from thereon [see: H. Rougler et al. (2007)].

This allows the Cro-Magnon to retain its relative privileged place in human paleontological record of Europe, as likely ancestors of contemporary Europeans. However, while Cro-Magnon ties have been insinuated in northern Africa [see: here], few references to human paleontological record, if any, have actually been made that directly tie the so-called "Middle East" and possibly even Central Asia—the two main alternatives generally referenced within "Western" academia, with regards to the corridor for the peopling of Europe with anatomically modern humans—to the Cro-Magnon remains of Europe.

While not the most popular of ideas out there, there is nevertheless a theory entertained by some, that the Gibraltar Strait could have served as the alternative plausible passage through which the Cro-Magnon type made its way into the European subcontinent. This naturally, would place the African continent as the direct source of the population. It must be said however, other than some analysts from the past saying that late Paleolithic or early Holocene African specimens carry "Cro-Magnon-like" qualities about them, no material has been offered to the present author's awareness, that places "Cro-Magnon" specimens—presumably virtually indistinguishable from those of European paleontological record—on the African continent. This to remind readers, is a minimal link or connection that is yet to be made with "Middle Eastern" paleontological record. Notwithstanding, at least one effort seems to encourage the passage through the "Middle Eastern" corridor, as least, in so far as some observers are concerned: Caramelli et al.'s (2003) mitochondrial DNA investigations!

Paglicci-25 has the following motifs: +7,025 AluI, 00073A, 11719G, and 12308A. Therefore, this sequence belongs to either haplogroups HV or pre-HV, two haplogroups rare in general but with a comparatively high frequencies among today's Near-Easterners (35).

Caramelli et al. (2003) report that their findings suggest "Cro-Magnon" phylogenetic ties to contemporary groups of Europe, with certain nucleotide clusters indicating placement of their "Cro-Magnon" specimens' mtDNA into the hg N macrohaplogroup but just not under any known preexisting downstream sub-clades. From this, they conclude that while the "Cro-Magnon" mitochondrial DNA affinities to members of hg N erase any doubt about their inclusion into anatomically modern humans, the precise phylogenetic location amongst and relationship with contemporary groups remains elusive to them:

It is difficult to say whether the apparent evolutionary relationship between Paglicci-25 and Paglicci-12 and those populations is more than a coincidence. Indeed, the haplogroups to which the Cro-Magnon type sequences appear to belong are RARE among modern samples, and therefore their frequencies are poorly estimated.

In fact, to drive this point about their "Cro-Magnon" specimens being part of the very same phylogeny as recent humans, Caramelli et al. (2003 & 2008) make it a point to emphasize that they had no trouble amplifying their "Cro-Magnon" mtDNA segments using primers used to amplify those of recent human groups and determine the sequences thereof, unlike the case with Neanderthal mtDNA segments, which would not amplify using those primers, largely because Neanderthal DNA sequences are radically different from recent human examples.

This same phenomenon would ensure elimination of undetected contamination of Neanderthal DNA as opposed to the "Cro-Magnon" example, which is more prone to contamination with recent human DNA from the laboratory DNA handlers or handlers of the skeletal specimens. It is precisely because of the possibility of the latter, that Caramelli et al. (2003 & 2008) go to great lengths to extensively brief their readers on the highly stringent precautionary measures that they undertook in handling the specimens in extracting the DNA from the skeletal specimens, and in the case of the Paglicci-23 specimen, right from the excavation stage through to the laboratory storage and DNA extraction stages. They write:

Even the most stringent available criteria for validating ancient human DNA sequences DO NOT ALLOW ONE TO PROVE that the sequences determined are AUTHENTIC.

But that...

Only if a sequence is radically different from modern ones, as is the case for Neandertals, can one be relatively sure that no contamination has affected the results. Therefore, a certain degree of prudence is necessary before drawing any conclusions from this study. Still, none of the biochemical tests we carried out suggests that different sequences (namely the endogenous one plus some contaminating sequences) were amplified from the 23,000- and 25,000-year-old specimens that we used. In addition, the amino acid racemization test strongly suggests that reasonably well preserved DNA should be present in those specimens. Because DNA from all four Cro-Magnon type bone fragments could be amplified and sequenced only by using primers specific for modern humans, and not for Neandertals, there is little doubt that the mtDNAs of early a.m.h. and of cronologically close Neandertals were, at least, very different. - Caramelli et al. (2003)

It is of note that the Cambridge Reference Sequence (CRS) uses sequences of the Paglicci-23, uncovered by DNA sequencing performed by the same researchers mentioned above [once again, perhaps something overlooked by many but as a matter of observation, it is interesting how a European paleontological specimen is placed at the center against which the phylogenetic place of human mitochondrial markers worldwide are determined, esp. considering that Europe was one of the more recent landmasses to be effectively inhabited by anatomical modern humans/a.m.h. [the Americas being the other; the only land masses reporting relatively later dates of a.m.h. habitation]. This referential DNA data has since been used by multiple research teams to unlock the mysteries of recent human mitochondrial DNA network, and so, authenticity of this data thereof cannot be understated. This serves as incentive for Caramelli and his team to reassure readers of this crucial authenticity.

It would seem that Caramelli et al.'s findings, as it relates to removing any doubts about the "Cro-Magnons" being one of "us" (anatomically modern humans), is meant to place the burden of proof on those who promote the idea of Neanderthal gene flow finding its way into early modern human forebearers of recent Europeans. In fact, Caramelli et al.(2008) explicitly put that challenge to potential proponents of such an idea. One such proponent that comes to mind, is Erik Trinkaus in his work, European early modern humans and the fate of Neanderthals, 2007.

One might well have come across commentary about certain early modern human specimens featuring some or another "archaic", or what some call "plesiomorphic", feature about it; well, "Cro-Magnon" specimens have not escaped such characterizations. Common examples of this are references to the "large cranial capacity" of "Cro-Magnon" specimens and/or reported values of "robusticity" of the remains, which are generally claimed to produce mean values that are relatively greater than average recent human means.

Trinkaus tells us for example, that prominent occipital buns are a relatively rare sight in his Gravettian sample, but the "Cro-Magnon" specimens of that bunch seem to be the exception to this, along with other specifically named specimens therein. In other words, this presumably recurring feature places the likes of the "Cro-Magnon" as relative outliers amongst the Gravettian bunch:

Occipital buns are less common than among the EEMHs. However, prominent ones are present in 18.9% (n 37) of the individuals, including Brno 2, Cro-Magnon 3, Dolnı´ Ve˘stonice 11, Pavlov 1, and Prˇedmostı´ 1, 2, and 7. In addition, hemi-buns are present in 29.7% of the sample.

"Cro-Magnon 3" is implicated above, but what to make of say, Cro-Magnon I specimen, or some other so-called example? Will it bear out that the latter will show more prominent occipital bun than say, recent human specimens, where prominent occipital buns are also generally determined to be a rare sight? Let's find out. Here is a side profile of Cro-Magnon 1, the first "Cro-Magnon" specimen to be uncovered and found in France.

And now compare the above cranium with the Neanderthal example [left] and recent human right [Polynesian; right]:

Click on the image for greater resolution.

While there is an obvious greater sloping (angle) [and hence, less rounded-profile] of the posterior parietal bone on the Neanderthal skull, and henceforth—a more protruding occipital bun, that seen on the recent human example on the other hand, is relatively understated. So, how does that of the Cro-Magnon 1 specimen above fare with that of recent human cranium; any marked differences in the manifestation of the occipital bones between the Cro-Magnon and the recent human example? Not much, that can be discerned from the given photographic profiles.

Obviously, if the Cro-Magnon 1 specimen does not have the prominent occipital bun as that pointed out by Trinkaus, about his Cro-Magnon 3 specimen, then there is obvious physical variation going on here. Is it any wonder therefore, that Trinkaus explains off his observations around such cranial elements as "polymorphic" across the designated "types" under study; that is to say, he seizes on the variation in pattern of the cranial trait at hand, to conveniently push forward the case for Neanderthal gene flow into early modern European human groups?

The idea here, is to say that gene flow explains the inconsistency of pattern around a cranial element at hand within the designated early modern human examples under study, rather than be interpreted as a function of possible autochthonous intra-population or intra-group diversity. This is precisely the sort of mentality that Caramelli et al. (2003 & 2008)—through their uniparental DNA findings—sought to finally put to rest, or at the very least, place the burden of proof on the leading proponents. Fact is, and as pointed out here before, many crania from Europe—dating back to more or less contemporaneous time frames [the so-called Gravettian period in this case]—have been blanketly called "Cro-Magnon", as though they constitute a "type", predicated on certain superficial skeletal similarities across them, even though there are visible variations amongst them as well.

Take the following example, of yet another cranium called "Cro-Magnon" [to the right], recovered in Czech territory, Brno, along side a Neanderthal skull [left]:

Click on the image for greater resolution.

The above cranium is obviously incomplete, but a close inspection of the frontal bone suggests that there is a somewhat mild supraorbital ridge, by no means as prominent as that of the Neanderthal specimen beside it. This specimen does seem to also have some emphasized occipital bun, although again here, the posterior of the Neanderthal's parietal bone is more slanted and less rounder than the so-called Cro-Magnon specimen. One might say that Caramelli et al.'s (2003) DNA findings for example, around Paglicci-23, Paglicci-25 and Paglicci-12, all of them dubbed as "Cro-Magnons", could suggest close inter-specimen phylogenetic relationship, and hence, could make a case for treating "Cro-Magnon" as a "type". But even here, only three specimens are dealt with, and while there are reportedly close mitochondrial DNA affinities between them at certain loci, they also reportedly fall into different and unique but also yet-to-be-determined branches. For instance, the Paglicci-25 sample is claimed to have mtDNA motifs which suggest affiliation with the eitherPre-HVorHV haplogroup (which split to give rise to haplogroups H and V), which are all part of the N macro-haplogroup. This failure to specify strict placement of the Paglicci-25 clade into a singular well-defined clade is perhaps an indication of the kind of ambiguity the authors are dealing with...

To recap: Paglicci-25 has the following motifs: +7025 AluI, 00073A, 11719G, and 12308A. Therefore, this sequence belongs to either haplogroups HV or pre-HV, two haplogroups rare in general but with a comparatively high frequencies among today's Near-Easterners (35).

The indecision characterizing Caramelli et al.'s (2003) inference of the Paglicci-25 sequences belonging to either hg pre-HV or or hg HV, primarily stems from the reported motifs of 73A and 11719G. With markers tagged as "hg pre-HV" [now dubbed "hg R0"] having already been attributed with both 11719G motif and the 73A motif [not to leave out the reported Alu insertion], it made/makes little sense to be indecisive about where to place a clade with both motifs, especially in the face of coming up short of downstream markers that are supposed to define hg HV.The information around pre-HV clades and the 11719G motif came out by ca. 2000, when Richards et al. point out...

By use of restriction digestion with the enzymes HaeIII and Tsp509I, the former in conjunction with a mismatched primer, the status at nucleotide positions 11719 and 11251, respectively, was checked in 12 mtDNAs harboring the motif 16126C-16362C, which, until now, had been a cluster with an ambiguous position in the mtDNA phylogeny (Macaulay et al. 1999), being either pre-HV or pre-JT. All samples bore the 11719G (+11718HaeIII) mutation that is characteristic of HV (Saillard et al., in press), whereas none of them bore the 11251G (–11251Tsp509I) mutation that is characteristic of JT (Hofmann et al. 1997; Macaulay et al. 1999). Thus, these mtDNAs were shown to constitute an early branch in the pre-HV cluster. - Richards et al., Tracing European Founder Lineages in the Near Eastern mtDNA Pool, 2000.

It should be noted that 73A itself is not relegated to hg R0 (formerly hg pre-HV) or some of its subclades; it has been linked to the African hg L1a as well. This leaves the 11719G allele [along with the given Alu insertion] providing a stronger case for hg R0. The 12308A motif has not been identified in either hg R0/pre-HV or hg HV. On the other hand, the Paglicci-12 sample shows affiliation with any of the mentioned N sub-haplogroups, according to Caramelli et al. (2003), which were:

Thus, the rather limited nucleotide information given to us about these specimens above essentially makes them paraphyletic clades of their own. The authors, for example, extrapolate that the Paglicci-12 mtDNA falls into the Hg N clade from a single mutation at the nucleotide position "16233":

Following the definition given in ref. 36, the presence of a single mutation in 16,223 within HRVI suggests a classification of Paglicci-12 into the haplogroup N*, which is observed today in several samples from the Near East and, at lower frequencies, in the Caucasus (35).

This extrapolation itself is suggestive of rush to judgment, since in of itself, the mutation at position 16223 (C to T) says very little about the phylogenetic position of the Paglicci specimen. Mutations at that same position are reported in for example, the entire L3 macrohaplogroup, including members of haplogroup M like M1a3, M7b, M7c3, M27. So, one would have to go for a lot more than that, in the event of which, the other loci information provided the authors may well be necessary to examine: We were told that motifs 00073G, 10873C, 10238T suggest familial association with hg N. Said mutations at both positions 73 and 10873 are again invoked in hg L3, not to mention hg L1 and hg L2 [see, information on position 10873 in hg M here, for instance], which therefore tells us little about the rationality of the special emphasis on these loci. Interestingly, the following critique had been offered in response, courtesy of Hans-J. Bandelt (2005)...

It was asserted that specimen Paglicci-25 is identical to rCRS and Paglicci-12 differs from rCRS by a transition at 16223 in HVS-I. According to the authors, specific mtDNA sites outside HVS-I were also analysed ('by amplification, cloning, and sequencing of the surrounding region'), but no details were given in the paper, except reporting that Paglicci-25 has -7025 AluI and bears nucleotides A at 73, G at 11719, and A at 12308, whereas Paglicci-12 shows G at 73, C at 10873, T at 10238, and AACC at 10397–10400. These additional analyses were only carried out in one lab and not duplicated in a second lab. The authors further asserted that the mtDNA of both specimens belong to typical Near Eastern haplogroups. In particular, the mtDNA of specimen Paglicci-12, with claimed mutations at sites 73, 10873, and 16223 but none in the stretch 10397–10400relative to rCRS, was regarded as a member of haplogroup N. They have, however, confused the roles of C and T at 10873 in the mtDNA phylogeny – in fact, C at both sites 10400 and 10873, as observed in Paglicci-12, indicates that this mtDNA haplotype should rather not belong to either of the Eurasian/Oceanian haplogroups M and N, which completely cover the non-African mtDNA pool.

Yes, with regards to that last point in particular, the locus data that Caramelli et al. (2003) report for position 10873 is inconsistent with that reported elsewhere for hg N. Hg N has been implicated with a transition carrying T at 10873, in say the following for example,...

Analysis of position 10873 (the MnlI RFLP) revealed that all the M molecules (eastern African, Asian and those sporadically found in our population surveys) were 10873C (Table 3). As for the non-M mtDNAs, the ancient L1 and the L2 African-specific lineages5, as well as most L3 African mtDNAs, also carry 10873C.

Although not specifically named above, the bulk of autochthonous non-M mtDNA markers of non-Africans fall under hg N branch of the superhaplogroup L3. Therefore, hg N is tacitly implicated here as being characterized by a C to T transition at 10873. Hg M on the other hand, continues to carry the 10873C state. So perhaps, Hans-J. Bandelt could have attained more precision here, by emphasizing this bit of unsaid information, because otherwise his piece above would leave the unsuspecting reader to misleadingly draw the conclusion that hg M does NOT carry the 10873C motif, when it in fact does. This emphasis is warranted, particularly when one considers that Bandelt himself was a participant to the very Quintana-Murci et al. (1999) above, along with Semino. On the other hand, it would be correct to note that hg M bears T at 10400 instead of C, as noted above; that being the case, then all in all, the obvious conclusion is that Bandelt has correctly observed that Caramelli et al.'s reporting should serve as a red alert not to place the Paglicci-12 DNA into hg N or hg M respectively on the basis of these DNA sites. In summary, this is how it needs to be said:

As Bandelt notes, the transition C at 10400 should rule out Paglicci-12's phylogenetic place under hg M. It thereby follows, that while the 10400C motif may not necessarily rule out the possibility that the Paglicci-12 mtDNA lineage could fall under hg N [since the Alu insertion 10397 or 10400 C to T site doesn't exist in hg N] or any other non-M clade for that matter, it doesn't allow any logical inference of the specimen's place particularly under hg N either. Conversely, while not adequate on its own enough to precisely place the phylogenetic position of Paglicci-12 in the mtDNA network, the reporting of 10873C from Paglicci-12 sequences alone, does not rule out its placement in hg M either, but it does however, rule out its placement in hg N, in a direct contrast to what Caramelli et al. (2003) reported. So, if the sequences of these Paglicci specimens don't logically place them in either hg M or hg N, then what does that leave us with? This question will shortly be revisited.

As for the mutation carrying T at 10238 on the Paglicci-12 mtDNA, it should be noted that the examples generally invoked within hg N, say hg I and subclades of hg N1a, are said to bear a mutation carrying C at 10238. A transitional mutation at this position has been implicated in hg B4a, speaking of which as a matter of simple interest, in Silva et al.'s (2002) study, a Japanese hg B mtDNA was reported to have one of a deletion instead of a transition but that had been written off elsewhere as a case of 'phantom mutation' or else a 'missense mutation' [Hans-J. Bandelt et al. (2003), Yong-G. Yao et al. (2003)]; in simple words, sequencing error and report thereof.

Notwithstanding the issues surrounding the proposed phylogenetic propositions of Caramelli et al. (2003), if one were to entertain the possibility that the Paglicci specimen sequences are indeed long drifted-out rare hg N markers, and that the various paleontological specimens dubbed as "Cro-Magnon" represented a "type", then it may well serve the purpose of placing the Cro-Magnon type as likely ancestors of recent European groups. The presence of Hg N markers in the so-called "Near East" could lend support to the use of the "Near Eastern" corridor in the peopling of the European subcontinent, an idea that will undoubtedly sit well with those who prefer "Near Eastern" origin of the so-called Cro-Magnon.

While still at hypotheticals, a case can be made thereof, however, that such prospect can open up the possibility that the Cro-Magnon types miscegenated with groups in the migration route through such a corridor, in what could have possibly involved several step migrations encompassing movement from Africa [presumably of a male-biased nomadic group] onto the "Middle East" and then onto Europe.To this end, there are others yet, who argue that this does not rule out an ultimate or even direct African origin for the "Cro-Magnon".

Naturally, all these opposing ideological camps tacitly treat "Cro-Magnon" as a type. Advocates amongst this last group propose the Gibraltar Strait as the likely route for a direct passage from Africa into the European sub-continent. When confronted with reports like say, Caramelli et al.'s (2003), about the phylogenetic placement of the "Cro-Magnon" lying somewhere in hg N, elements of this last group respond with studies that invoke hg N clades on the African continent. One example of this, is reference to Sarah Tishkoff et al.'s 2007 publication, History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation.

Here, hg N had been linked to elements across essentially all the major language groups on the African continent; namely, Khoisan, Niger-Kordofanian, Nilo-Saharan and Afrisan (Afro-Asiatic). While much commentary has been made in previous journals about hg N presence in eastern Africa, few references are ever made with regards to "sub-Saharan" western Africa. Citing previous journals, this study takes hg N as far west as Nigeria and Guinea. Now, when hg N is spoken of in African context, more often than not, it is generally explained off as likely the outcome of back-migration. Think for example, Richards et al. (2003) or Kivisild et al. (2004). Both these publications profess that the eastern African examples of hg N, including its subclade of hg pre-HV, are likely relics of back-migration from the so-called "Near East", while at the same time, pointing out how intriguingly rare say, Ethiopian examples are in the "Near East".

Interestingly, given the geographical position of Ethiopia and the history of the region with southern Arabia, one might be tempted to reckon that it would make perfect sense if Ethiopians closely shared "Near Eastern" markers with the Yemeni more than folks of any other location in "southwestern Asia". But the noted research teams have come to find out, that this is not the case. Kivisild et al. (2004) for instance note that,...

Despite the fact that haplogroup-N lineages occur at equally high frequency in Ethiopians and Yemenis, only three haplotypes (representing 3% of the total Yemenisample) werefound to match between the two populations. This suggests that the immediate source populations for these lineages in the Near East, from which they derive, could have been different. - Kivisild et al. 2004

Indeed, hg N does have a substantial presence in Africa, as do variants of hg M. Can all these therefore be simply written off as back-migration? It is worth investigating, if momentarily. Much of hg N presence on the African continent has thus far been largely been reported in eastern African areas, the region of Africa, putting coastal northern Africa aside, that interestingly seems to get the most attention from research teams from the "West".

Notwithstanding the relative marginal attention that "sub-Saharan" western Africa gets from "Western" research teams, hg N has reported that far out on the continent! Never mind the huge swaths of territory in between, like Chad and surrounding areas thereof, that virtually get little to no attention when it comes to sampling. One would assume that this area would be one of a significant interest, given its central position in the Sahara and Sahel, and hence, its intra-continental corridor significance. Yet, it has recently been found, as earlier hinted by the paraphyletic hg R Y-chromosomes in Cameroon, that this very area is host to more hg R chromosomes!

Had a lot of observers paid attention to this fact, questions and erroneous suppositions around the likely origin of the hg R-rich Sudanese Fulani sample reported in Hassan et al.'s (2008) study would have been kept to a minimum. If haplogroups like R can be found in substantial frequencies in this intriguingly understudied region, and equally interesting, as rare as their molecular status are, could such trends not be replicated in sections of mtDNA gene pool of that region as well?

While one comes out from reading Kivisild et al. (2004) that elements of eastern African hg N could have been derived from northeastern areas, other patterns are not easily explained by this, and interestingly, neither explained off by gene flow from southern Arabia; an example of this observation has been just cited above. To demonstrate this phenomenon, let's take a look at several markers, starting with the mtDNA markers, since thus far, attempt has been to place the "Cro-Magnon" phylogenetically mainly from a maternal or mitochondrial DNA standpoint:

Hg N

Lineages that belong to haplogroup N that cover virtually all mtDNA sequences in western Eurasia (Richards et al. 2000) show substantial frequencies both in the Yemeni (44%) and Ethiopian (31%) mtDNA pools. In this respect, Ethiopians differ explicitly from most other sub-Saharan African populations studied thus far. Within Ethiopia, the frequency of N lineages is significantly higher (P<.05) in samples that originate from its northern territory (48%), which was the center of the Aksum kingdom, than among other Ethiopians, mostly originating from the south-central part of the country (27%). At the same time, there was no significant difference in the proportions of haplogroup N between the Semitic and Cushitic linguistic groups in our sample—for example, between Amharas and Oromos.

Thus, the lineage is not structured along linguistic lines, but rather geographical cline. As we go through other markers, we'll see a pattern wherein one senses that these markers were very likely heavily clustered in the central-eastern Sahel area as the Ogolian aridity began to retreat, and river systems slowly began to fill up again, which nomadic groups took advantage of amongst others. Given the intense aridity in the Ogolian period, the Sahara would have been for the most part unideal for permanent habitation, and hence, not likely the period wherein one would expect most of the clades described herein to be heavily clustered. The southern boundary of the Sahara would have been as noted here before, extended beyond its current one, hence, forcing previous Saharan groups to seek refuge in areas beyond said boundary. The major clades of Hg E likely emerged in these areas in the then more southward Sahel and nearby areas beyond; however, with the letting up of the Ologian aridity, movements of groups carrying these clades began to take place along with the northward-shifting of the Sahel and retreating boundary of the Sahara within the continent. We see archaeological signs of such movements taking place from ca.15 to 13 ky ago. This seems to be the period during which movements into the Levant take place, involving hg E clades, but reading on, the big picture continues to unravel...

Hg N1a

N1a is a minor mtDNA haplogroup that has been observed at marginal frequencies in European, Near Eastern, and Indian populations (Mountain et al. 1995; Richards et al. 2000). It occurs at a significant frequency in both Ethiopian and Yemeni populations. Six Ethiopian N1a lineages, restricted to Semitic-speaking subpopulations, show low haplotype diversity and include an exact HVS-I sequence match with a published N1a sequence from Egypt (Krings et al. 1999). A related sequence, from southern Sudan (Krings et al. 1999), was misclassified as a member of the L1a clade (Salas et al. 2002). Yemeni N1a sequences, on the other hand, display a high level of haplotype (h=0.89) and nucleotide (ρ=2.75±1) diversity, combined with the highest frequency (6.9%) of this haplogroup reported so far.

We see that the Ethiopian sequences show their closest matches with those of northern areas of Africa than with those in southern Arabia and the "Near East" and elsewhere, where as noted, save for Yemen, hg N1a markers are visibly lower than in Ethiopian populations.

hg pre-HV

Haplogroup (preHV)1 is by far the most frequent (10.4%) subclade in the Ethiopian N cluster (fig. 2B). The majority of the Ethiopian (preHV)1 lineages match or derive from founder haplotypes common to Near Eastern, southern Caucasian, and North African populations (Krings et al. 1999; Metspalu et al. 1999; Richards et al. 2000; Kivisild et al. 2003b). Previously, the highest frequency (20.4%) of (preHV)1 lineages was observed in Yemeni Jews (Richards et al. 2003), significantly higher than their frequency in our Yemeni non-Jewish sample (3.4%; P<.01). This probably reflects strong genetic drift in the founding population of Yemeni Jews. Because (preHV)1 lineages occur in populations of the Near East, the Caucasus, and Mediterranean Europe—where African L0-L6 lineages are absent or rare—it is more likely that their presence in East Africa reflects a back-migration from the Near East rather than an in situ origin of (preHV)1 in Ethiopia (Richards et al. 2003). Nevertheless, we notice that several Ethiopian (preHV)1 lineages, including (1) variants with a transversion at np 16305, (2) HVS-I motif 16126-16309-16362, and (3) HVS-I motif 16126-16172-16184A-16362, were not found in 185 (preHV)1 sequences sampled from >20,000 individuals from Arabia, the Near East, and Europe (Macaulay et al. 1999; Metspalu et al. 1999; Richards et al. 2000; authors' unpublished data), except for an HVS-I haplotype 16126-16305T-16362 that occurs (12.5%) in Ethiopian Jews (Thomas et al. 2002). Their elevated frequency and uniform presence among major language groups in Ethiopia (table 1) suggests that these derived lineages may represent a relatively old introgression of lineages to the Ethiopian mtDNA pool from the Near East.

Again, northern Africa is implicated. One confronts a situation wherein Ethiopian examples fail to find matches with those in the "Near East" or southern Arabia, and again, there doesn't seem to any structuring along linguistic lines. Furthermore...

...A specific haplotype match in haplogroup (preHV)1—which is also widely spread in the Near East—between Ethiopian Jews and non-Jews is more problematic, because it is also possible that the non-Jews obtained the lineage from the Jews. This particular (preHV)1 haplotype, with a rare transversion at np 16305, (1) has not been detected, so far, among other Semitic populations of the Near East; whereas, (2) in Ethiopia, it occurs both among Cushitic and Semitic speakers; and, (3) in Ethiopian Jews, there are many sub-Saharan African lineages from haplogroups L0–L3. It is more likely, therefore, that the matching haplotype does not represent the incursion of Jewish maternal lineages into the Ethiopian gene pool but that this haplotype instead substantiates the extent of Ethiopian admixture in the Falasha population. Taken together, the influx of the elements of the Hebraic culture in the first centuries a.d. probably did not have a major impact on the genetic pool of Ethiopians, and the present-day Jews of Ethiopian descent probably assimilated genes from the local non-Jewish populations through conversion of the latter to Judaism. The other two episodes of intrusion of Semitic influence, related to contacts with southern Arabia, are weakly supported by our data. This is because, among the haplogroup N lineages present in high frequency in the Tigrais and other Ethiopian ethnic groups, only a few revealed close relationships with equivalent lineages present in southern Arabia.

Again, very few matches with south Arabian examples, an area from where some presume proto-Semitic could have diffused into the African horn! This is significant, considering the geographical proximity.

Note that earlier in the passage pertaining to hg preHV, it was reckoned that the said marker probably reflects back-migration mainly on the account of hg L markers being relatively rare in the so-called "Near East", Caucasus and "Mediterranean Europe". Later on, however, one runs into this:

Third, the high frequency of haplogroup L6 in Yemenis points to an enigmatic link between the southwestern Arabian gene pool with that of East Africa. This haplogroup derives from the phylogenetic tree of sub-Saharan African mtDNA haplogroups but shows only marginal incidence in Ethiopians and is completely absent elsewhere in Africa. Its high frequency in Yemen, together with low haplotype diversity, probably reflects the effect of genetic drift in a small founding population. A recent bottleneck of the general Yemeni population seems unlikely because of the high haplotype variation in other haplogroups (table 3). A founder effect from outside is also not supported, because of the lack of a possible source population outside Yemen, in whom the L6 founder haplotype would be present at a significant frequency.

From the present evidence, the possibility cannot be eliminated that this haplogroup may even have originated from the same out-of-Africa migration that carried haplogroups M and N and founded the mtDNA diversity of Eurasia, the Americas, and Oceania. Yet, this scenario would imply a total isolation of a southern Arabian population from the others in that region to explain the absence of L6 types in other populations of the Near East, Arabia, and elsewhere in the world. Alternatively, in consideration of the highly heterogeneous haplogroup composition of individual populations from East Africa (e.g., from Tanzania [Knight et al. 2003]) and the almost complete lack of data from some regions (like Somalia and Kenya), it is possible that the source population of Yemeni L6 varieties has not yet been sampled.

Indeed, there are huge swaths of African territory that are inexplicably ignored, when their otherwise obvious significance is considered. Research teams from the "West" just can't seem to get around with fixating on certain areas of Africa, and drawing questionable conclusions from fragmentary data. For instance, with its strategic location between Ethiopia and Egypt, one would think that gathering genetic data in Sudanese territory would be on the priority list, as has been noted earlier with regards to the Chadic area, but Sudan is in fact astonishingly understudied. It is hard to imagine one getting a complete picture of the relationship of populations in say, the African horn and Egypt, without considering that in between, which happens to be Sudan. Now, having explained off substantial presence of hg N markers in Ethiopian groups as likely the outcome of back-migration, merely on the account that hg L markers are rare in "Near East", Caucasus and "Mediterranean Europe", the authors are forced to openly recognize the likelihood of hg L markers leaving the continent along with the ancestral clades of those seen in those very non-African locations. What is the significance of this? The obvious: the rare prevalence of hg L in said territories cannot be offered as unequivocal proof that hg N clades found in Ethiopian groups are relics of back-migration.

Continuing with our examination...

hg H

When the fact that haplogroup H is the predominant subclade of N in most western Eurasian populations is considered, its frequency in Ethiopians is surprisingly low (0.7%). Among the three haplogroup H lineages found, one Tigrai carried a characteristic HVS-I transition at np 16218, which has been observed in haplogroup H lineages—mostly in those of Near Eastern origin, but also in two Yemeni H sequences and two Assiut sequences from Egypt (Krings et al. 1999; Richards et al. 2000).

Why the relatively lower incidence of hg H in Ethiopian groups is cause for surprise is anyone's guess, considering that up until now, considerable instances of mismatches with not only "Near Eastern" examples have been reported, but also with south Arabian examples. Once again, the fact that a northern African territory is named, cannot be ignored in the final analysis. And from the language used here, one cannot help but draw the conclusion that the remaining hg H markers must therefore be examples that are distinct from those located elsewhere.

Hg J

Three of the five haplogroup J lineages in Ethiopians share a distinct HVS-I motif, 16069-16126-16193-16300-16309 (J1c), that is characteristic of J sequences in populations from the southern Caucasus, the Near East, and North Africa (Di Rienzo and Wilson 1991; Richards et al. 2000; Brakez et al. 2001; Maca-Meyer et al. 2001; Plaza et al. 2003). In East Africa, J1c sequences have been found in one Datoga from Tanzania (Knight et al. 2003) and in one Gurna from Egypt (Stevanovitch et al. 2004). The other two Ethiopian J sequences, present in Tigrais, belonged to a subclade of J2 that is defined by a transition at np 6671 (Herrnstadt et al. 2002). Most of the Yemeni J sequences, in contrast, share the combination of 16145 and 16261 mutations in haplogroup J1b, which is a common motif of J lineages in populations from the Near East and all over western Eurasia (Richards et al. 2000).

Once again, northern African territory has been implicated, in J1c distribution, and once again, rare subclades are reported for the Ethiopian groups. Not to be left out, is the recurring contrasting-patterns between the Ethiopian samples and those of Yemeni counterparts.

hg T

All Ethiopian and Yemeni haplogroup T sequences clustered with either T1 or T2 subclades, consistent with the classification of all existing European T coding-region sequences (Ingman et al. 2000; McMahon et al. 2000; Finnilä et al. 2001; Herrnstadt et al. 2002; Coble et al. 2004). One Amhara T sequence, however, which harbors a transition at np 14233, characteristic of T2 sequences, lacked the other substitution at np 11812, present in all other Ethiopian and European T2 sequences. The np 11812 substitution was similarly absent in a complete North African T sequence (Maca-Meyer et al. 2001). The Tigrai T1a sequence matches a Kerma sequence from Nubia (Krings et al. 1999), whereas the Amhara T1b sequence shows a mutation at np 16320 on top of the common founder haplotype in the Near East (Richards et al. 2000). Five of the six T2 sequences detected among Amhara and Tigrai samples shared a transition at np 16292 that is widespread in the haplogroup T context in Europe, the Near East, and North Africa. However, the two Tigrai T2 sequences share a combination of four downstream HVS-I mutations (fig. 2B) that have not been reported elsewhere.

...so continues the trend of rare clades in Ethiopian samples. Still, another connection made with northern African territory is shown, around a clade that is rare outside of African territory.

With that, we conclude the first half of this post here. Continue reading here, for the conclusion in the second half. Go here (click) for the conclusion.

1 comment:

The Big Valley
said...

Indeed, there are huge swaths of African territory that are inexplicably ignored, when their otherwise obvious significance is considered. Research teams from the "West" just can't seem to get around with fixating on certain areas of Africa, and drawing questionable conclusions from fragmentary data. For instance, with its strategic location between Ethiopia and Egypt, one would think that gathering genetic data in Sudanese territory would be on the priority list, as has been noted earlier with regards to the Chadic area, but Sudan is in fact astonishingly understudied. It is hard to imagine one getting a complete picture of the relationship of populations in say, the African horn and Egypt, without considering that in between, which happens to be Sudan. Now, having explained off substantial presence of hg N markers in Ethiopian groups as likely the outcome of back-migration, merely on the account that hg L markers are rare in "Near East", Caucasus and "Mediterranean Europe", the authors are forced to openly recognize the likelihood of hg L markers leaving the continent along with the ancestral clades of those seen in those very non-African locations. What is the significance of this? The obvious: the rare prevalence of hg L in said territories cannot be offered as unequivocal proof that hg N clades found in Ethiopian groups are relics of back-migration.

Great point. Too often is sampling skewed when it comes to studying African peoples. And a magisterial write-up overall. Keep pouring it on!

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